AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_ctra_reg_100.orf -o174_ctra_100.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCT00118	300	Chlamydia_trachomatis

Motif number 1

ATGCAACATGTTCTACTCTGTCCTATATGCAGA	1	26	0	TTCTCTCTTC	    0.993579	-275
CCCAAAGCGATTCTGCACTGCGCAGACAAGAAT	1	102	0	TTCTCACTCC	    0.962291	-199
CTCTATCCTCCTTTTCTCTTTACATACATTTCA	1	147	0	CTTTCTCTTC	    0.992101	-154
GAACTAAGAGTTTCCCTCTATCCTCCTTTTCTC	1	162	0	TTTCCTCTTC	    0.993579	-139
ATAATTGCCATTGTACACTCTCCTTCTTATCGT	1	202	1	TTGTCACTTC	    0.978292	-99
GGTCAAAAATTTTAACCCTCTACGATAAGAAGG	1	223	0	TTTACCCTTC	    0.962345	-78
     GGCCTCTTCTCTCATTTCCTTCTGTAGA	1	283	0	CTTCCTCATC	    0.955787	-18
          **** **** * *

Masking position 2
Map Score:   5.96139

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 151
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

TTTCGTATCGCCAATGCAACATGTTCTACT	1	42	0	CCAATGCAAC	     0.98011	-259
ATTGGCGATACGAAAGCACTGATTGCTATG	1	57	1	CGAAAGCACT	    0.978924	-244
TTGAATCCCTCCATAGCAATCAGTGCTTTC	1	68	0	CCATAGCAAT	    0.994842	-233
CAGGCACACCCCAAAGCGATTCTGCACTGC	1	114	0	CCAAAGCGAT	    0.992032	-187
GGAGAGTGTACAATGGCAATTATTTTTGGG	1	195	0	CAATGGCAAT	    0.966076	-106
          **********

Masking position 3
Map Score:   3.6503

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 72
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

CAACATGTTCTACTCTGTCCTATATGCAGAA	1	25	0	TACTCTTCCT	    0.993243	-276
TATCCTCCTTTTCTCTTTACATACATTTCAC	1	146	0	TTCTCTTACA	    0.937873	-155
CTAAGAGTTTCCCTCTATCCTCCTTTTCTCT	1	161	0	CCCTCTTCCT	     0.99181	-140
ATTGCCATTGTACACTCTCCTTCTTATCGTA	1	205	1	TACACTTCCT	    0.973164	-96
TGTATGTGCGTCATCTCTACAGAAGGAAATG	1	268	1	TCATCTTACA	    0.919957	-33
      GGCCTCTTCTCTCATTTCCTTCTGT	1	286	0	TCTTCTTCAT	     0.90756	-15
          ****** ****

Masking position 6
Map Score:   2.80573

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 265
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

TGTCCTATATGCAGAAATTGATCGTTAATC	1	11	0	GCAGAAATTG	    0.927999	-290
CGATACGAAAGCACTGATTGCTATGGAGGG	1	62	1	GCACTGATTG	    0.961351	-239
TGCCTGTCGTGAAATGTATGTAAAGAGAAA	1	138	1	GAAATGTATG	    0.950283	-163
TAGTTCCCCAAAAATAATTGCCATTGTACA	1	189	1	AAAATAATTG	    0.776947	-112
CCACAAGATTGAAGTGTATGTGCGTCATCT	1	254	1	GAAGTGTATG	    0.977322	-47
CATCTCTACAGAAGGAAATGAGAGAAGAGG	1	279	1	GAAGGAAATG	    0.958406	-22
          **********

Masking position 3
Map Score:   0.538995

Number of sites scoring better than the average of aligned sites = 331
Number in coding regions = 331
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 7

          **********

No masking
Map Score:   7.91135e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0